Somatic sequence alterations in twenty-one genes selected by expression profile analysis of breast carcinomas

Abstract

Introduction: Genomic alterations have been observed in breast carcinomas that affect the capacity of cells to regulate proliferation, signaling, and metastasis. Re-sequence studies have investigated candidate genes based on prior genetic observations (changes in copy number or regions of genetic instability) or other laboratory observations and have defined critical somatic mutations in genes such as TP53 and PIK3CA.

Methods: We have extended the paradigm and analyzed 21 genes primarily identified by expression profiling studies, which are useful for breast cancer subtyping and prognosis. This study conducted a bidirectional re-sequence analysis of all exons and 5', 3', and evolutionarily conserved regions (spanning more than 16 megabases) in 91 breast tumor samples.

Results: Eighty-seven unique somatic alterations were identified in 16 genes. Seventy-eight were single base pair alterations, of which 23 were missense mutations; 55 were distributed across conserved intronic regions or the 5' and 3' regions. There were nine insertion/deletions. Because there is no a priori way to predict whether any one of the identified synonymous and noncoding somatic alterations disrupt function, analysis unique to each gene will be required to establish whether it is a tumor suppressor gene or whether there is no effect. In five genes, no somatic alterations were observed.

Conclusion: The study confirms the value of re-sequence analysis in cancer gene discovery and underscores the importance of characterizing somatic alterations across genes that are related not only by function, or functional pathways, but also based upon expression patterns.

Figure 1

Hierarchical clustering analysis of 194 breast tumor samples analyzed using the 'SAM264' patient survival associated gene set augmented with nine additional genes included in the resequencing analysis. (a) Hierarchical clustering overview that shows the overall context for the 21 genes. (b) Close up of the sample associated dendrogram, which identifies the tumor samples that were re-sequenced in red. (c) Luminal/ER⁺ epithelial gene set showing coordinated expression of ESR1, GATA3, FOXA1, and XBP1. (d) Proliferation gene set showing expression of STK6, MYBL2, and PLK1. (e) Basal epithelial gene set showing the expression of FOXC1 and FZD7. (f) The expression profiles of the additional genes that were re-sequenced but that did not fall into the previous expression patterns are shown, and their position in the larger cluster is also shown in panel a. All genes identified in red text were analyzed by re-sequencing in this study, and only FBXW7 and PIN1 were not included in this cluster analysis because their average expression levels did not meet the gene filtering criteria. ER, estrogen receptor.

Figure 2

Distribution of samples with observed number of somatic alterations. Total number of somatic alterations per sample are included underneath the bars and the total number of samples in each category is represented on the vertical axis.